MC3: Markov Chain conventional single edge proposal move

In anna-pacinkova/intomics_package: Integrative analysis of multi-omics data to infer regulatory networks

Markov Chain conventional single edge proposal move

Description

MC3 This function samples a conventional single edge proposal move.

Usage

MC3(
  source_net,
  omics,
  layers_def,
  B_prior_mat,
  beta.source,
  partition_func_UB_beta_source,
  parent_set_combinations,
  BGe_score_all_configs_node,
  annot
)

Arguments

source_net	list with adjacency matrix and other parameters needed for MCMC simulation.
omics	named list containing the gene expression (possibly copy number variation and methylation data). Each component of the list is a matrix with samples in rows and features in columns.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
B_prior_mat	a biological prior matrix.
beta.source	named list with hyperparameter beta value and other parameters needed for MCMC simulation.
partition_func_UB_beta_source	numeric vector the upper bound of the partition function needed to define the prior distribution of network structure.
parent_set_combinations	list of all possible parent set configuration for all nodes available.
BGe_score_all_configs_node	list of nodes BGe score for all possible parent set configurations.
annot	named list containing the associated methylation probes of given gene.

Value

List of 10 elements needed to define adjacency matrix

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
package="IntOMICS")
OMICS_mod_res <- OMICS_module(omics = omics, PK = PK, 
    layers_def = layers_def, TFtargs = TFtarg_mat, annot = annot, 
    r_squared_thres = 0.3, lm_METH = TRUE)
first.adapt.phase_net <- first_adapt_phase(omics = OMICS_mod_res$omics, 
    B_prior_mat = OMICS_mod_res$B_prior_mat, prob_mbr = 0.07,
    energy_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node,
    len = 5, layers_def = OMICS_mod_res$layers_def, 
    BGe_score_all_configs_node =
    OMICS_mod_res$pf_UB_BGe_pre$BGe_score_all_configs_node, 
    parent_set_combinations = OMICS_mod_res$pf_UB_BGe_pre$parents_set_combinations, 
    annot = OMICS_mod_res$annot)
MC3(B_prior_mat = OMICS_mod_res$B_prior_mat, 
    source_net = first.adapt.phase_net$nets[[length(first.adapt.phase_net$nets)]],
    layers_def =  OMICS_mod_res$layers_def, annot = OMICS_mod_res$annot,
    beta.source = first.adapt.phase_net$betas[[length(first.adapt.phase_net$betas)]], 
    partition_func_UB_beta_source = first.adapt.phase_net$partition_func_UB_beta_source, 
    omics = OMICS_mod_res$omics, 
    parent_set_combinations = OMICS_mod_res$pf_UB_BGe_pre$parents_set_combinations, 
    BGe_score_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$BGe_score_all_configs_node)

anna-pacinkova/intomics_package documentation built on Aug. 13, 2022, 11:38 a.m.